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        <H2>SpectraSelection</H2>
        <p align="justify">
            You can select which spectra to include in the
            PRIDE XML file. You have tree options:<br><br>

            <b>Simple Spectra Selection:</b> include either all spectra or
            all identified spectra.<br><br>
            <b>Advanced Spectra Selection:</b> Select all spectra where the (spectra) file name
            (partially) matches the list of provided names, or select all spectra where the
            identification id (the value in the ID column in the table) matches the list of provided ids. If more than one file name or id is
            given they have to be separated by the same separation character, which can be chosen
            by the user. To use new line (one file name per line) for separating, simply leave the
            separator field empty. Note that the selection is <b>case sensitive</b> when applied in this step,
            but <b>case insensitive</b> if applied without previewing. It is always recommended to verify
            that your selection is correct before continuing.
            <br><br>
            <b>Manual Spectra Selection:</b> Select the spectra to include by selecting or deselecting
            the spectra in the list. To use this option you first have to load the spectra by
            clicking the "Load Spectra" button.
            <br><br>
            If you want to preview the advanced spectra selection before continuing, you first have to
            load the spectra (by clicking the "Load Spectra" button) and then click the "Apply Selection"
            button. Clicking the "Apply Selection" button disables the simple spectra selection options.
            <br><br>
            There is also the possibility of setting a lower peptide threshold score. This means that
            only peptides above a given score are included in the PRIDE XML file.
            <br><br>
            Finally there is an option of using a protein identification filter to remove
            unwanted protein identifications. All protein identifications containing the text
            inserted into the "Protein Identification Filter" field, will be not be included
            in the PRIDE XML file.
            <br><br>
            For Mascot dat files you can also set a lower threshold for the confidence in the
            identifications. Only identifications with a confidence above the selected
            threshold will then appear in the PRIDE XML file. Use the spinner to select the
            value, or type in the desired value. Non-integer numbers must by typed in using
            period (".") as the decimal sign.
            <br><br>
            In this frame you can also add spectrum annotations. In order to do this you first
            need to load the spectra. Adding spectrum annotations is done by
            right clicking on the given row and inserting the details into the
            appearing dialog.
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